Sequence
atgc intronic sequence ATGC exonic sequenceTCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttctttctcgggaactcaaaagtcggtttttccattcttgcag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ20436 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os04g31070.1 (Oryza sativa), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagc-agagtttcttctttctcgggaactcaaaagtcggtttttcc-attcttgcag---------------------------------------
| ||||| ||| | || || ||||| | ||||| |||||||| || |||||||| ||||| |||||||| || || ||| |||| || ||||| ||||||||||| | | | || | | | | || |||| | | || ||
CAGGCATGGTGATCTTCTTAATAAGTACATGTACCTTACTGGACGTGTTGACATGAAACAAATTGAGAAGACAATACAATACCTGATTGGGTCTGGGATGgtaagagctaatatctatttaggcatgatgatattattttcctttttacttaagtttacaatgctattgtggataaccttgttatcaatagccatgtctc
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os02g30200.1 (Oryza sativa), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttctttctcgggaactcaaaagtcggttt--ttccattcttgcag-------------------------------------------
|| || ||||| || | |||||||| ||||||||||| || | |||||||||| ||| ||||||||||||| |||||| | || || || || |||||||| | || | || | || | |||||| ||| || || || |
CCGGCACGGCGACCTGATGAACAAGTACCTCTACCTCACCGGCAGGGTCGACATGAGGCAGGTCGAGAAGACGATACAGTACCTCATTGGCTCCGGCATGgtaagcatttgctccctccgtttc----accttacaagtcgctttgattttctttttctatttaaactttttaaagtttaattaagattatagaaaatattagc
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g69080.1 (Oryza sativa), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttctttctcgggaactcaa--aagtcggtttttccattcttgcag----------------------------------------
| ||||| || | || ||||| ||||||||||||||||| | || ||||||| ||||| |||||||| || ||||| | || || ||||||||||||| || ||| ||| | | | | | | | | ||| | |
CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagtttt-cttccgcttctttgctagcctagctatatttaactgattattttgaaattgtcattcatgagtttttccctcaagcaattgttttcctc
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G026793_T01 (Zea mays), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttct-----ttctcgggaactcaaaagtcggtttttccatt--cttgcag----------------------------------
| ||||| || | || || ||||| | ||||| |||||||| || |||||||| ||||| |||||||| || ||||| |||| ||||| ||||||||||| | | | || | | || | | | | || |||||||| || ||| ||
CAGACATGGTGACCTCCTTAATAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATTCAGTATCTGATTGGTTCCGGAATGgtaagcgattaagtactattatatatcttcaaggattttgatatctgtttttccctttccttccatttatagcttttcaatgaatcatgaaatcaccgac
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AC215690.3_FGT002 (Zea mays), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaag-agcagagtttcttctttctcgggaactcaaaagtcggtttttccattcttgcag----------------------------------------
| ||||| || | || |||||||| | ||||| |||||||| || |||||||| ||||| |||||||| || || || |||| ||||| ||||||||||| || | | || | || | || ||| ||
CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagttaaacactactggtatctgtctttcccttcccttccatttataactttcaatgggtcatgaaatcattcacatttttgcttttgataacca
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT3G02630.1 (Arabidopsis thaliana), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaaga---gcagagtttcttcttt-------ctcgggaactcaaaagtcggtttttccattcttgcag-------------------------------
| | ||||| ||| | || ||||||||||| || || |||| || || ||||||| ||| || || ||||| || |||||| |||| ||||||||||||||||| || | |||||| ||| | | | ||| || | ||| | | | | |
TAGACATGGGGATCTCCTTAACAAGTATCTTTATCTGTCTGGTCGGGTAGACATGAGGCAGATTGAAAAGACTATTCAGTACCTGATTGGTTCTGGAATGgtaagctctgctaactttcttttttgctttaacccataatctcctaaagttgcatttgcgctttaggaagtgactggggatggggatacaatcgttacat
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv00s0499g00030.t01 (Vitis vinifera), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttctttctcgg--gaactcaaaa--gtcggtttttccattcttgcag-------------------------------------
| | ||||| || | |||||||||||||| ||||| |||||||||| |||||||||||||| |||||||| || ||||| | || || || |||||||||||| | | || || ||| | || | | || | || | || || ||
TAGGCATGGTGACCTTCTCAACAAGTATCTTTACCTTTCTGGACGAGTAGACATGAAGCAAATTGAGAAGACAATTCAGTATCTCATAGGATCAGGAATGgtaagatcctaattcctacttatttggctgcatccactatcatcataaactatatactatgagtcttgtttcacagagaatgtaggaaaattttgccatt
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00580.t01 (Vitis vinifera), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaaga--------gca-gagtttcttctttctcgggaactcaaaagtcggtt----tttcca----ttcttgcag-----------------------------
| || || || | || || ||||||||||| || ||||| |||| |||||||| ||||||||||||||||| ||||| ||||| || |||||||||| ||| || | ||| || ||| | || |||| | | | || |||||| |
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgctttttttttttttttttttttctgtagtcaatcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00550.t01 (Vitis vinifera), 5'ss of exon 1
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagag------cagagtttcttctttctcgggaactcaaaagtcggtt----tttcca----ttcttgcag-----------------------------
| | || || | || || ||||||||||| || ||||| |||| |||||||| ||||||||||||||||| ||||| ||||| || |||||||||| ||| | | ||| ||| | || |||| || | | || |||||| |
CAGGGACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgcccttttttttttttttttctgtagtcagtcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00730.t01 (Vitis vinifera), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaaga--------gcagagtttctt----ctttctcgggaactcaaaagtcggtttttccattcttgcag-----------------------------
| || || || | || || ||||||||||| || ||||| |||| |||||||| ||||| ||||||||||||||||| ||||| | |||||||||| ||| ||| | ||| || ||| || || | | | | | ||| | | |
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATTGAGAAGACGATCCAGTATTTGATTAGGGCTGGAATGgtgagattcttgctgcatacttttttactgttttatctccaaaaccacaatatagtgacagattttggtaagacgtaaggtggatttgaaattgatacac
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00650.t01 (Vitis vinifera), 5'ss of exon 5
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaaga-----gcagagtttc--ttctttctcgggaactcaaaagtcggtt----tttcca----ttcttgcag-----------------------------
| || || || | || || ||||||||||| || ||||| |||| |||||||| ||||||| ||||||||| ||||| ||||| || |||||||||| ||| || | | || ||| | || |||| || | | || |||||| |
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGCGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatcccctttttttttttttttttctgtagtcagtcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00750.t01 (Vitis vinifera), 5'ss of exon 2
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaag------------agca----gagtttcttctttctcgggaactcaaa--agtcggtttttcca---ttcttgcag--------------------
| ||||| || | ||||||||||| || || || |||||||||| ||||||| ||||| |||||||| || || || ||||| || || ||||||||||| | || | | || | ||| ||| || ||| ||| || | ||| |
CAGGCATGGTGACCTTCTCAACAAGTACCTATATCTGTCTGGACGAGTAGACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttccttcacatgaacatttgaaaggttttatctctaaactactttaagcagttaaactttgcaaaacttttgaaatgaggaaatgatgggaggct
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00740.t01 (Vitis vinifera), 5'ss of exon 3
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaaga--------gcagagtttctt----ctttctcgggaactcaaaagtcggtttttccattcttgcag-----------------------------
| || || || | || || ||||||||||| || ||||| |||| || ||||| ||||| |||||||| |||||||| ||||| | |||||||||| ||| ||| | ||| || ||| || || | | | | | ||| | | |
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGATATGAAACAAATTGAGAAGACAATCCAGTATTTGATTAGGGCTGGAATGgtgagattcttgctgcatacttttttactgttttatctccaaaaccacaatatagtgacagattttggtaagacgtaaggtggatttgaaattgatagac
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttctttctcgggaactcaaaagtcggtttttccattcttgcag------------------------------------------
||||| || || |||| |||||||| | ||| | || || ||||| ||||||| |||||||||||||| || ||||||||||| || ||||| ||||||||| | | | ||| || || | | | | | ||| |||
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca-tgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa
upper sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S181_115V6.1 (Physcomitrella patens), 5'ss of exon 3
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagag-cagagtttcttctttctc----gggaactcaaa---agtcggtttttccat----tcttgcag---------------------------------------------------------------------------------------------------------------------------------
|||||| || ||| |||| ||||||||| | ||| | || || ||||| ||||||| ||| |||||||||| | |||||||||||| || ||||| ||||| |||| | | | || || || | || | | || ||||| || | |||| |
TCGTCACGGAGATCTGCTGAACAAGTATTTGTACTTGACAGGGCGAGTGGACATGAGACAAGTCGAGAAGACAACCCAGTACTTGATTGGATCTGGCATGgtgagagtctgtaatcctactgagtccagtgaaaaatgtagcgtgatctgttttaccgcatgcttttgctgtcataccctgctgctagactcggggtatcgaagaggcctgtaagtgtattgattgatgggtagaggtgttctgtagggtatcgatgttggagtgtgagaattgactttgaatattatttggtgttgcagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|169026093|gb|FE434484.1|FE434484EST: ACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATG GATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcag ... attcttgcagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTC
EST:
gi|169083162|gb|FE493767.1|FE493767EST: ACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATG GATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcag ... attcttgcagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTC
EST:
gi|169104261|gb|FE503701.1|FE503701EST: ACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATG GATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcag ... attcttgcagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTC
EST:
gi|169056947|gb|FE465472.1|FE465472EST: ACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATG GATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcag ... attcttgcagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
32 (upstream exon),
33 (downstream exon)
Score:
13TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcag ... attcttgcagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTCCAGGAGCGAGCCACCGCCATCTCTCATGGCAACACTGCTCGCCACGCCA
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Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttctttctcgggaactcaaaagtcggtttttccattcttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA